Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,108,247	T→C	33.6%	T6T (ACT→ACC)	kbaY →	tagatose 6‑phosphate aldolase 1, kbaY subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,108,247	0	T	C	33.6%	89.9 / 67.1	119	T6T (ACT→ACC)	kbaY	tagatose 6‑phosphate aldolase 1, kbaY subunit
Reads supporting (aligned to +/- strand): ref base T (44/35); new base C (28/12); total (72/47)
Fisher's exact test for biased strand distribution p-value = 1.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.51e-01

Only 100 of 119 total aligned reads displayed.

CAAGGCGTAATCATTCATCCGTGGCAGGCATAAGAGGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAT  >  minE/2108185‑2108307

cAAGGCGTAATCATTCATCCGTGGCAGGCATAAGAGGATCGCATTATGAGCATTATCTCCACTAAatat                                                        >  1:806688/1‑69 (MQ=255)

            attcatCCGTGGCAGGCATAAGAGGATCGCATTATGAGCATTATCTCCACTAAATATCTGt                                                    >  1:2645675/1‑61 (MQ=255)

               catCCGTGGCAGGCATAAGAGGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGcc                                         <  1:2984303/69‑1 (MQ=255)

                     tGGCAGGCATAAGAGGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGcc                                   <  1:1163832/69‑1 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGccc                                        >  1:2278149/1‑55 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCATGCCAATGGcacc                          >  1:892347/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCATGCCAATGGcacc                          >  1:379639/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:1604758/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:1033367/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:1979174/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:1992694/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:2061014/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:2297560/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:2390787/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:2424098/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:2867388/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:3263974/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:473386/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:712817/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:928125/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:946214/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:1577526/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:147214/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:1309475/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcac                           >  1:3062197/1‑66 (MQ=255)

                              tAAGAGGATCGCATTATGAGCATTATATCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGcacc                          >  1:848953/1‑66 (MQ=255)

                               aaGATGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:572339/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:2672032/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:1645790/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:1046422/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:1724158/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:286953/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:1212295/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:2474641/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:3395110/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:380021/69‑1 (MQ=255)

                               aaGAGGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:485053/69‑1 (MQ=255)

                               aaGACGATCGCATTATGAGCATTATCTCCACCAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         <  1:1939945/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCTCTAAATATCTGTTACa                                                <  1:1533883/45‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTa                                                  <  1:2040244/43‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTa                                                  <  1:2983350/43‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTa                                                  <  1:1766536/43‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACa                                                <  1:2072160/45‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACa                                                <  1:2867063/45‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACa                                                >  1:3289074/1‑45 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACa                                                <  1:901974/45‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACa                                                >  1:2373678/1‑45 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACa                                                >  1:2601181/1‑45 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:2790245/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1033753/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:1120923/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:706046/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:3004669/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:3007821/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:702184/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:3181068/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:1157564/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:545164/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:538077/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:1145256/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1729779/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:2722615/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:2660608/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1730335/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:2475959/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1334091/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:2763818/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1461530/1‑69 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:2339946/69‑1 (MQ=255)

                                agagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcg                         >  1:1523001/1‑68 (MQ=255)

                                 gagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTa                                                  <  1:974706/42‑1 (MQ=255)

                                 gagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:2109571/68‑1 (MQ=255)

                                 gagGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:1496736/68‑1 (MQ=255)

                                   ggATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGTCCAATGGCTACGCGGt                     <  1:115376/69‑1 (MQ=255)

                                   ggATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGt                     <  1:399908/69‑1 (MQ=255)

                                   ggATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGt                     <  1:924737/69‑1 (MQ=255)

                                      tCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1028017/1‑63 (MQ=255)

                                      tCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:2366017/1‑63 (MQ=255)

                                      tCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        >  1:1126940/1‑63 (MQ=255)

                                        gCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTg                <  1:2152597/69‑1 (MQ=255)

                                        gCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTg                <  1:1607695/69‑1 (MQ=255)

                                          aTTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGcc                                   <  1:162800/48‑1 (MQ=255)

                                           ttATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAcgc                        <  1:385209/58‑1 (MQ=255)

                                             aTGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCtttt           >  1:3003705/1‑69 (MQ=255)

                                                aGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAAc        >  1:941214/1‑69 (MQ=255)

                                                aGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAAc        >  1:1319357/1‑69 (MQ=255)

                                                aGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAAc        >  1:770350/1‑69 (MQ=255)

                                                aGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAAc        >  1:1915122/1‑69 (MQ=255)

                                                aGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAAc        >  1:1364609/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTAc                          >  1:51706/1‑45 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACAtt     >  1:3374060/1‑66 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:1666051/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:2008573/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:7177/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:713564/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:1875535/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:1906540/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:1419765/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:2339985/1‑69 (MQ=255)

                                                      aTCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAt  >  1:2754540/1‑69 (MQ=255)

CAAGGCGTAATCATTCATCCGTGGCAGGCATAAGAGGATCGCATTATGAGCATTATCTCCACTAAATATCTGTTACAGGACGCCCAGGCCAATGGCTACGCGGTGCCTGCTTTTAACATTCAT  >  minE/2108185‑2108307

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A